def __init__(self,
residue,
mon_lib_srv,
rotamer_manager,
sin_cos_table,
target_map=None,
unit_cell=None,
backbone_sample=True,
accept_only_if_max_shift_is_smaller_than=None):
adopt_init_args(self, locals())
#
if(target_map is None):
assert not backbone_sample
assert unit_cell is None
# Initial state
rotamer_start = rotamer_manager.rotamer(residue=self.residue)
sites_cart_start=self.residue.atoms().extract_xyz()
if(target_map is not None):
target_start = self.get_target_value(sites_cart=sites_cart_start)
# Actual calculations
self.chi_angles = self.rotamer_manager.get_chi_angles(
resname=self.residue.resname)
co = mmtbx.refinement.real_space.aa_residue_axes_and_clusters(
residue = self.residue,
mon_lib_srv = self.mon_lib_srv,
backbone_sample = True)
if(backbone_sample):
self.fit_c_beta(c_beta_rotation_cluster = co.clusters[0])
self.fit_side_chain(clusters = co.clusters[1:])
# Final state
if(target_map is not None):
rotamer_final = rotamer_manager.rotamer(residue=self.residue)
target_final = self.get_target_value(
sites_cart=self.residue.atoms().extract_xyz())
# Sanity and consistency check
#XXX not always hold due to approx fast math assert rotamer_final != "OUTLIER"
# Potentially this will keep an OUTLIER if no better fit found
if(target_start > target_final):
self.residue.atoms().set_xyz(sites_cart_start)
def __init__(self,
residue,
mon_lib_srv,
rotamer_manager,
sin_cos_table,
vdw_radii=None,
xyzrad_bumpers=None,
target_map=None,
target_map_for_cb=None,
unit_cell=None,
backbone_sample=True,
accept_only_if_max_shift_is_smaller_than=None):
adopt_init_args(self, locals())
#
if(target_map is None):
assert not backbone_sample
# Initial state
rotamer_start = rotamer_manager.rotamer(residue=self.residue)
sites_cart_start = self.residue.atoms().extract_xyz()
self.co = mmtbx.refinement.real_space.aa_residue_axes_and_clusters(
residue = self.residue,
mon_lib_srv = self.mon_lib_srv,
backbone_sample = True)
if(target_map is not None):
target_start = self.get_target_value(sites_cart = sites_cart_start)
# Actual calculations
self.chi_angles = self.rotamer_manager.get_chi_angles(
resname = self.residue.resname)
if(len(self.co.clusters)>0):
if(backbone_sample):
self.fit_c_beta(c_beta_rotation_cluster = self.co.clusters[0])
self.fit_side_chain(clusters = self.co.clusters[1:])
# Final state
if(target_map is not None):
target_final = self.get_target_value(
sites_cart=self.residue.atoms().extract_xyz())
if(target_start > target_final):
self.residue.atoms().set_xyz(sites_cart_start)